GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Azospirillum brasilense Sp245

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, acs
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
alanine braC, braD, braE, braF, braG
arabinose gguA, gguB, chvE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
arginine braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, put1, putA
asparagine ans, bztA, bztB, bztC, bztD
aspartate bztA, bztB, bztC, bztD
cellobiose bgl, mglA, mglB, mglC, glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
deoxyribose deoP, deoK, deoC, adh, acs
ethanol etoh-dh-nad, adh, acs
fructose fruA, fruI, 1pfk, fba, tpi
fucose fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate dctA
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntA, gntB, gntC, gntK, gnd
glucose mglA, mglB, mglC, glk
glucose-6-P uhpT
glucosamine SLC2A2, glc-kinase, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate braC, braD, braE, braF, braG, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
D-lactate lctP, glcD, glcE, glcF
L-lactate lctP, lutA, lutB, lutC
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctA
maltose susB, mglA, mglB, mglC, glk
mannitol PLT5, mt2d, scrK
mannose manP, manA
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagEcba, nagA, nagB
2-oxoglutarate Psest_0084, Psest_0085
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
proline AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
propionate lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
pyruvate dctM, dctP, dctQ
rhamnose rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
ribose rbsU, rbsK
D-serine cycA, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol SOT, sdh, scrK
succinate dctA
sucrose ams, mglA, mglB, mglC, glk
threonine braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
thymidine nupG, deoA, deoB, deoC, adh, acs
trehalose treF, mglA, mglB, mglC, glk
tryptophan aroP, tnaA
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol fruI, x5p-reductase
xylose xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory